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JacksonH44
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PPI-prediction
MIT License
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Fill in type stubs and flesh out docs for src/data
#73
JacksonH44
closed
1 month ago
0
Delete files
#72
JacksonH44
closed
1 month ago
0
Delete unneccessary files
#71
JacksonH44
closed
1 month ago
0
Make project Windows compatible
#70
JacksonH44
closed
1 month ago
0
Add linting support for Windows and src/visualization
#69
JacksonH44
closed
1 month ago
0
Add Docker option for collecting frustration stats
#68
JacksonH44
opened
1 month ago
0
Add test data
#67
JacksonH44
closed
1 month ago
0
Address pytest warnings
#66
JacksonH44
opened
1 month ago
0
collect_stats throws an error with certain complexes
#65
JacksonH44
closed
1 month ago
1
Generate more consistent documentation
#64
JacksonH44
closed
1 month ago
0
Ensure Windows OS compatibility
#63
JacksonH44
closed
1 month ago
0
Fix bug with non-existent MSA directory when running ColabFold
#62
JacksonH44
closed
1 month ago
0
run_colabfold cannot make MSA directory
#61
JacksonH44
closed
1 month ago
0
Add frustration features, integrate with overall stats, and improve ColabFold stats collection
#60
JacksonH44
closed
1 month ago
0
Add CI linting support for src/visualization
#59
JacksonH44
closed
1 month ago
0
CI linting on Windows returns OSError
#58
JacksonH44
closed
1 month ago
0
Plot feature relationship figures
#57
JacksonH44
closed
1 month ago
0
Create descriptive visualizations of the dataset so far
#56
JacksonH44
closed
1 month ago
0
Do not use monomer model ranking
#55
JacksonH44
closed
1 month ago
0
Integrate surface area statistics into collection
#54
JacksonH44
closed
1 month ago
0
Compute surface area statistics across all models
#53
JacksonH44
closed
2 months ago
0
Calculate average surface area change across all models, not across all residues
#52
JacksonH44
closed
2 months ago
0
Get frustration matrix features
#51
JacksonH44
closed
1 month ago
1
Extract richer features from ColabFold metrics
#50
JacksonH44
closed
2 months ago
0
Generate richer structural features from ColabFold outputs
#49
JacksonH44
closed
2 months ago
0
Cache poetry dependencies to speed up CI workflow testing
#48
JacksonH44
closed
2 months ago
0
Optimize CI pipeline
#47
JacksonH44
closed
2 months ago
0
Calculate delta surface area metrics
#46
JacksonH44
closed
2 months ago
0
Calculate change in surface areas
#44
JacksonH44
closed
2 months ago
0
Generate contact maps from PDB files
#43
JacksonH44
closed
2 months ago
0
Find residues involved in interaction site
#42
JacksonH44
closed
2 months ago
0
Generate contact maps from PDB files
#41
JacksonH44
closed
2 months ago
0
Pre-process ColabFold data for HPC and collect stats from ColabFold structures
#40
JacksonH44
closed
2 months ago
0
Pre and Post Process ColabFold data
#39
JacksonH44
closed
2 months ago
1
Set up and call folding script pipeline
#38
JacksonH44
closed
2 months ago
0
Create sorted file of complex lengths and visualize lengths distribution
#37
JacksonH44
closed
2 months ago
0
Generate report of lengths of proteins and protein complexes
#36
JacksonH44
closed
2 months ago
1
Add functionality to run Colabfold for observations in the dataset
#35
JacksonH44
closed
2 months ago
0
Update .gitignore
#34
JacksonH44
closed
3 months ago
0
Add positive and negative PPI datasets
#33
JacksonH44
closed
3 months ago
0
Filter datasets for only protein complexes that will have <2,000 amino acids
#32
JacksonH44
closed
3 months ago
0
Preprocess pairs of MSA files into a single ColabFold-compliant file format
#31
JacksonH44
closed
3 months ago
0
Filter datasets for complexes with less than ~2000 amino acids
#30
JacksonH44
closed
3 months ago
0
Preprocess MSAs into LocalColabFold-compliant format
#29
JacksonH44
closed
3 months ago
0
fix(msas): revert uniref30 filter on dataset (#24)
#28
JacksonH44
closed
3 months ago
0
Download MSA from OpenProteinSet s3 bucket
#27
JacksonH44
closed
3 months ago
0
Map NCBI Gene Symbols to SwissProt IDs
#26
JacksonH44
closed
3 months ago
0
Download file from MSA s3 Bucket
#25
JacksonH44
closed
3 months ago
0
Find MSAs for all dataset observations
#24
JacksonH44
closed
2 months ago
0
Filter dataset for only those proteins with a canonical transcript
#23
JacksonH44
closed
3 months ago
0
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